Job ID = 6507834 SRX = SRX494836 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:24:17 prefetch.2.10.7: 1) Downloading 'SRR1198368'... 2020-06-26T13:24:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:24:59 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:24:59 prefetch.2.10.7: 'SRR1198368' is valid 2020-06-26T13:24:59 prefetch.2.10.7: 1) 'SRR1198368' was downloaded successfully Read 5595479 spots for SRR1198368/SRR1198368.sra Written 5595479 spots for SRR1198368/SRR1198368.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:18 5595479 reads; of these: 5595479 (100.00%) were unpaired; of these: 127527 (2.28%) aligned 0 times 4499829 (80.42%) aligned exactly 1 time 968123 (17.30%) aligned >1 times 97.72% overall alignment rate Time searching: 00:01:19 Overall time: 00:01:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 319552 / 5467952 = 0.0584 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 22:28:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 22:28:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:28:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:28:52: 1000000 INFO @ Fri, 26 Jun 2020 22:28:59: 2000000 INFO @ Fri, 26 Jun 2020 22:29:05: 3000000 INFO @ Fri, 26 Jun 2020 22:29:12: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 22:29:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 22:29:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:29:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:29:19: 5000000 INFO @ Fri, 26 Jun 2020 22:29:20: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:29:20: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:29:20: #1 total tags in treatment: 5148400 INFO @ Fri, 26 Jun 2020 22:29:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:29:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:29:20: #1 tags after filtering in treatment: 5148400 INFO @ Fri, 26 Jun 2020 22:29:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:29:20: #1 finished! INFO @ Fri, 26 Jun 2020 22:29:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:29:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:29:20: #2 number of paired peaks: 423 WARNING @ Fri, 26 Jun 2020 22:29:20: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Fri, 26 Jun 2020 22:29:20: start model_add_line... INFO @ Fri, 26 Jun 2020 22:29:20: start X-correlation... INFO @ Fri, 26 Jun 2020 22:29:20: end of X-cor INFO @ Fri, 26 Jun 2020 22:29:20: #2 finished! INFO @ Fri, 26 Jun 2020 22:29:20: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 22:29:20: #2 alternative fragment length(s) may be 4,46,494,509,563 bps INFO @ Fri, 26 Jun 2020 22:29:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.05_model.r WARNING @ Fri, 26 Jun 2020 22:29:20: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:29:20: #2 You may need to consider one of the other alternative d(s): 4,46,494,509,563 WARNING @ Fri, 26 Jun 2020 22:29:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:29:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:29:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:29:22: 1000000 INFO @ Fri, 26 Jun 2020 22:29:28: 2000000 INFO @ Fri, 26 Jun 2020 22:29:30: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:29:34: 3000000 INFO @ Fri, 26 Jun 2020 22:29:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:29:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:29:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.05_summits.bed INFO @ Fri, 26 Jun 2020 22:29:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (556 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:29:40: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 22:29:46: 5000000 INFO @ Fri, 26 Jun 2020 22:29:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 22:29:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:29:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:29:46: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:29:46: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:29:46: #1 total tags in treatment: 5148400 INFO @ Fri, 26 Jun 2020 22:29:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:29:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:29:46: #1 tags after filtering in treatment: 5148400 INFO @ Fri, 26 Jun 2020 22:29:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:29:46: #1 finished! INFO @ Fri, 26 Jun 2020 22:29:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:29:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:29:47: #2 number of paired peaks: 423 WARNING @ Fri, 26 Jun 2020 22:29:47: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Fri, 26 Jun 2020 22:29:47: start model_add_line... INFO @ Fri, 26 Jun 2020 22:29:47: start X-correlation... INFO @ Fri, 26 Jun 2020 22:29:47: end of X-cor INFO @ Fri, 26 Jun 2020 22:29:47: #2 finished! INFO @ Fri, 26 Jun 2020 22:29:47: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 22:29:47: #2 alternative fragment length(s) may be 4,46,494,509,563 bps INFO @ Fri, 26 Jun 2020 22:29:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.10_model.r WARNING @ Fri, 26 Jun 2020 22:29:47: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:29:47: #2 You may need to consider one of the other alternative d(s): 4,46,494,509,563 WARNING @ Fri, 26 Jun 2020 22:29:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:29:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:29:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:29:52: 1000000 INFO @ Fri, 26 Jun 2020 22:29:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:29:59: 2000000 INFO @ Fri, 26 Jun 2020 22:30:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:30:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:30:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.10_summits.bed INFO @ Fri, 26 Jun 2020 22:30:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (336 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:30:06: 3000000 INFO @ Fri, 26 Jun 2020 22:30:12: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:30:19: 5000000 INFO @ Fri, 26 Jun 2020 22:30:20: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:30:20: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:30:20: #1 total tags in treatment: 5148400 INFO @ Fri, 26 Jun 2020 22:30:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:30:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:30:20: #1 tags after filtering in treatment: 5148400 INFO @ Fri, 26 Jun 2020 22:30:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:30:20: #1 finished! INFO @ Fri, 26 Jun 2020 22:30:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:30:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:30:20: #2 number of paired peaks: 423 WARNING @ Fri, 26 Jun 2020 22:30:20: Fewer paired peaks (423) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 423 pairs to build model! INFO @ Fri, 26 Jun 2020 22:30:20: start model_add_line... INFO @ Fri, 26 Jun 2020 22:30:20: start X-correlation... INFO @ Fri, 26 Jun 2020 22:30:20: end of X-cor INFO @ Fri, 26 Jun 2020 22:30:20: #2 finished! INFO @ Fri, 26 Jun 2020 22:30:20: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 22:30:20: #2 alternative fragment length(s) may be 4,46,494,509,563 bps INFO @ Fri, 26 Jun 2020 22:30:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.20_model.r WARNING @ Fri, 26 Jun 2020 22:30:20: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:30:20: #2 You may need to consider one of the other alternative d(s): 4,46,494,509,563 WARNING @ Fri, 26 Jun 2020 22:30:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:30:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:30:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:30:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:30:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:30:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:30:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494836/SRX494836.20_summits.bed INFO @ Fri, 26 Jun 2020 22:30:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (140 records, 4 fields): 1 millis CompletedMACS2peakCalling